2.1. DNA and RNA
Deoxyribonucleic acid (DNA) is the primary genetic material of most organisms. Ribonucleic acid (RNA) is the primary genetic material in certain viruses. Additionally, a form of RNA known as messenger RNA (mRNA) is found in all cells and comprises copies of portions of the primary genetic information found in the DNA. In its natural state, DNA is found in the form of a pair of complementary chains of nucleotides which are interconnected as a double helix (see FIG. 1). A nucleotide in turn is composed of a nitrogenous base (see FIGS. 2 and 3), which identifies the nucleotide, linked by an N-glycosidic bond to a five-carbon sugar. RNA differs from DNA in that in DNA the nucleotide sugar is deoxyribose, while in RNA, the sugar is ribose. A phosphate group serves to link the nucleotides together, forming the backbone of a single strand of DNA (see FIG. 2). Normally, the nitrogenous base is one of the following: adenine, guanine, thymine and cytosine (respectively denoted A, G, T, and C), or uracil (U) in place of thymidine in RNA (see FIG. 3). The order of the four nucleotides, A, G, T and C, in the chain is often referred to as the sequence of the DNA and can be specified simply by setting down the symbols A, G, T and C in the order in which these four nucleotides appear in the DNA strand.
The two chains (or strands) of a DNA double helix are held together by hydrogen bonding between the nitrogenous bases of their individual nucleotides. This hydrogen bonding is specific in that adenine in one strand must pair with thymine (or uracil in RNA) in the other strand, and guanine with cytosine. The sequence of bases in one strand of DNA is thus complementary to the sequence on the other strand.
A DNA chain has polarity: one end of the chain has a free 5'-OH (or phosphate) group (termed "the 5' end") and the other a free 3'-OH (or phosphate) group ("the 3' end"). By convention, the nucleotide sequence is written or read left-to-right in the direction from the 5' end to the 3' end. The two strands of a DNA double helix have opposite polarities. Thus the 5' end of one strand pairs with the 3' end of the other strand and the complementarity of the two strands is revealed by comparing one strand read in the 5' to 3' direction with the other strand read in the 3' to 5' direction.
Genetic information is encoded in the particular sequence (order of occurrence) of nucleotides along a DNA molecule and DNA sequencing is the process of determining that order in a particular DNA molecule.